Guide RNAs were designed by manual inspection of the genomic sequences flanking rs2277862, rs10889356, and rs10872142 and evaluated for potential off-target activity using the CRISPR Design tool at http://crispr.mit.edu. Protospacers were cloned into the BbsI site of pGuide (Addgene plasmid #64711) via the oligonucleotide annealing method, and, if not already present, a G was added to the 5′ end to facilitate U6 polymerase transcription. Genome editing was performed using pCas9_GFP (Addgene plasmid #44719), which co-expresses a human codon-optimized Cas9 nuclease and GFP via a viral 2A sequence. To generate the targeting construct for minor allele knock-in at rs10889356, 500-bp homology arms flanking a TTAA site 200 bp upstream of rs10889356 were amplified from genomic DNA (from the H7 hPSC line)—with the 3′ arm undergoing PCR-based mutagenesis to introduce the rs10889356 minor allele—and subcloned into the PB-MV1Puro-TK vector (Transposagen), which harbors a piggyBac transposon containing a puromycin selection cassette, to make PB-rs10889356. For CRISPRi studies, pAC154-dual-dCas9VP160- sgExpression (gift from Dr. Rudolph Jaenisch, Addgene plasmid #48240), a dual expression construct that expresses dCas9-VP160 and sgRNA from separate promoters, was modified by PCR-based
